Even if we interpret Cabinet Office minister Francis Maude's move as a distinct break with tradition, should we be alarmed? Photograph: Jeff Overs/BBC/PA

Imagine if Francis Maude realised his dreams of suzerainty over top Whitehall appointments – he or the prime minister would get final cut on the choice of permanent secretary.

Would that be the end of the world, or at least the end of Northcote-Trevelyan and the principle of civil service neutrality?

Let's pass over the observation that Whitehall seems to get much more exercised about changes to its norms and perks than about the often highly dubious and constitution-threatening policies it implements on behalf of ideology-driven ministers.

A first response to the concern expressed by the Civil Service Commission has to be: don't ministers already have the final say, de facto? Look what happened in November with the top job at Energy and Climate Change. Number 10 squashed the recommendation, approved by a panel led by Lord Stern and Sir Bob Kerslake. The result is that the whole appointments procedure will have to be repeated, spending constraints and the age of austerity be hanged.

Even in the olden, golden days, ministers who did not get on with their permanent secretaries could and did move them. In his diaries, Richard Crossman tells of insisting on getting rid of a permanent secretary he didn't like. Under John Major, Sir Peter Kemp, the inventor of Next Step agencies, was vetoed by ministers when a deserved promotion was due. More recently, the then cabinet secretary Lord Gus O'Donnell responded to a relationship problem by moving Sir Peter Housden out of Communities and Local Government.

Even if we interpret Maude's move as a distinct break with tradition, should we be alarmed? Won't he seek to fill permanent secretary roles with ideological soulmates or yes people?

Our response should be: let him try.

We are at only the dawn of the age of austerity. On the back of the autumn statement the Institute for Fiscal Studies estimates most departments, other than health, education and international aid, will have to cut their budgets by at least a third between 2010 and 2017. Getting there, even partially, will demand leadership, courage and deep technical skills. A Tory lookalike as permanent secretary is simply not going to hack it.

If you were Michael Gove, would you want as your permanent secretary a mandarin like Chris Wormald or some partisan plucked from a Tory thinktank, as you force through a thousand job cuts in the Department of Education while dismantling a system of schools administration and replacing it with a risk-prone, ramshackle arrangement of academy governing boards and direct accountability to a shrunken centre?

The likelihood is that neither the mandarin nor the partisan will avoid administrative catastrophe, but Wormald's knowledge of the system is surely not just the safer bet but the one more likely to realise the politician's aims.

You would have to be deeply cynical to suggest ministers would prefer anarchy to pushing through their programmes – and anarchy would be the probable outcome of appointing a permanent secretary who was merely a ministerial pet.

If Maude wins this fight, the victim won't be efficient and effective management in Whitehall, at least not at first. Civil service conventions, including appointments, have long needed re-examination.

No, the big loser will be the duumvirate of Kerslake and Sir Jeremy Heywood and the idea that Whitehall tapers to a tip, at which sits a cabinet secretary and a titular head of service, whether those roles are singular or plural.

Perhaps this is Maude's real objective: to break up one source of inertia in the central government system. Once Kerslake loses his sway over permanent secretary appointments, the very existence of his job becomes questionable.